Gurpreet Singh wrote:
Gurpreet Singh wrote:
> Dear Gromacs Users,
>
> I am using g_sas program of gromacs to calculate SASA, ?using
-pbc flag.
> It seems to me that the program does not take into account the
periodic
> boundary conditions.
> Even thought this problem is mentioned in the mailing list, it
still not
> clear whether the program can or cannot take into account the
> periodicity.
> i am using gromacs3.3.2 . Could anyone please clarify this.
>
http://bugzilla.gromacs.org/show_bug.cgi?id=180
I downloaded the gromacs 3.3.3 and carried out some test
calculations. The PBC is still not working, at least with test i
have performed.
I generated a trajcetory file containing two atoms in a cubic box of
4nm having same x and y coordinates and varied the z coordinates of
one of the atoms.
one atom is fixed at z coordinate of 3.9. The result of sasa vs
coordinates is as follows:
Step no z coordinate total_sasa
1 2.05000000074506 14.1497
2 2.10000000149012 14.1497
3 2.15000000223517 14.1497
4 2.20000000298023 14.1497
5 2.25000000372529 14.1497
6 2.30000000447035 14.1497
7 2.35000000521541 14.1497
8 2.40000000596046 14.1497
9 2.45000000670552 14.1497
10 2.50000000745058 14.1497
11 2.55000000819564 14.1497
12 2.60000000894070 14.1497
13 2.65000000968575 14.1497
14 2.70000001043081 14.1497
15 2.75000001117587 14.1497
16 2.80000001192093 14.1497
17 2.85000001266599 14.1497
18 2.90000001341105 14.1497
19 2.95000001415610 14.1497
20 3.00000001490116 14.1497
21 3.05000001564622 14.1497
22 3.10000001639128 14.1497
23 3.15000001713634 14.1497
24 3.20000001788139 14.1497
25 3.25000001862645 14.1497
26 3.30000001937151 14.1497
27 3.35000002011657 13.7971
28 3.40000002086163 13.1359
29 3.45000002160668 12.5849
30 3.50000002235174 11.9237
31 3.55000002309680 11.3727
32 3.60000002384186 10.7115
33 3.65000002458692 10.1605
34 3.70000002533197 9.49926
35 3.75000002607703 8.94826
36 3.80000002682209 8.39726
37 3.85000002756715 7.51566
38 3.90000002831221 14.1497
39 3.95000002905726 7.51566
40 2.980232238769531E-008 14.1497
41 5.000003054738045E-002 14.1497
42 0.100000031292439 14.1497
43 0.150000032037497 14.1497
44 0.200000032782555 14.1497
45 0.250000033527613 14.1497
46 0.300000034272671 14.1497
47 0.350000035017729 14.1497
48 0.400000035762787 14.1497
49 0.450000036507845 14.1497
50 0.500000037252903 14.1497
51 0.550000037997961 14.1497
52 0.600000038743019 14.1497
53 0.650000039488077 14.1497
54 0.700000040233135 14.1497
55 0.750000040978193 14.1497
I used the following command to calculate the sasa
g_sas_d -f test.xtc -s topol.tpr -pbc -ndots 500
I can attached the tpr and xtc file if needed
Please reopen the bugzilla and send your input there.
With Regards,
Gurpreet singh
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David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
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